PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G62090.2
Common NameBHLH132, EN111, PIF6, PIL2, T17J13.50
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family bHLH
Protein Properties Length: 363aa    MW: 40546.8 Da    PI: 6.5134
Description phytochrome interacting factor 3-like 2
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G62090.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH24.16.4e-08194238655
                  HHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   6 nerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                  n  Er+ R++iN+++ +L+ llP++      K +  ++L +A++Y+ +Lq
  AT3G62090.2 194 NSPERNQRNDINKKMRTLQNLLPNS-----HKDDNESMLDEAINYMTNLQ 238
                  778*********************8.....699**************998 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd000837.37E-8184242No hitNo description
Gene3DG3DSA:4.10.280.101.5E-11185251IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474592.75E-13187257IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088812.779188237IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PfamPF000109.1E-6194238IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.2E-6194243IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010017Biological Processred or far-red light signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000293anatomyguard cell
PO:0009005anatomyroot
PO:0009047anatomystem
PO:0020100anatomyhypocotyl
Sequence ? help Back to Top
Protein Sequence    Length: 363 aa     Download sequence    Send to blast
MMFLPTDYCC RLSDQEYMEL VFENGQILAK GQRSNVSLHN QRTKSIMDLY EAEYNEDFMK  60
SIIHGGGGAI TNLGDTQVVP QSHVAAAHET NMLESNKHVD DSETLKASSS KRMMVDYHNR  120
KKIKFIPPDE QSVVADRSFK LGFDTSSVGF TEDSEGSMYL SSSLDDESDD ARPQVPARTR  180
KALVKRKRNA EAYNSPERNQ RNDINKKMRT LQNLLPNSHK DDNESMLDEA INYMTNLQLQ  240
VQMMTMGNRF VTPSMMMPLG PNYSQMGLAM GVGMQMGEQQ FLPAHVLGAG LPGINDSADM  300
LRFLNHPGLM PMQNSAPFIP TENCSPQSVP PSCAAFPNQI PNPNSLSNLD GATLHKKSRK  360
TNR
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible251245_at0.0
Expression AtlasAT3G62090-
AtGenExpressAT3G62090-
ATTED-IIAT3G62090-
Functional Description ? help Back to Top
Source Description
TAIRencodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family.
Function -- GeneRIF ? help Back to Top
  1. PIF6 is expressed strongly during seed development, and two splice variants exist.
    [PMID: 19911288]
  2. PTB misexpression changes Alternative splicing (AS) of PHYTOCHROME INTERACTING FACTOR6, coinciding with altered rates of abscisic acid-dependent seed germination.
    [PMID: 23192226]
  3. The ability of Glc to induce IAA biosynthesis was upregulated in the pif1 pif3 pif4 pif5 quadruple mutant line compared with the wild type.
    [PMID: 23209113]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G62090.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Interaction ? help Back to Top
Source Intact With
IntActSearch Q8L5W7
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G62090
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB4936610.0AB493661.1 Arabidopsis thaliana At3g62090 mRNA for hypothetical protein, partial cds, clone: RAAt3g62090.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001078329.10.0transcription factor PIF6
SwissprotQ8L5W70.0PIF6_ARATH; Transcription factor PIF6
TrEMBLC0SVF80.0C0SVF8_ARATH; Putative uncharacterized protein At3g62090 (Fragment)
STRINGAT3G62090.20.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP25816128
MalvidsOGEM134231425
Publications ? help Back to Top
  1. Makino S,Matsushika A,Kojima M,Yamashino T,Mizuno T
    The APRR1/TOC1 quintet implicated in circadian rhythms of Arabidopsis thaliana: I. Characterization with APRR1-overexpressing plants.
    Plant Cell Physiol., 2002. 43(1): p. 58-69
    [PMID:11828023]
  2. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
    [PMID:12679534]
  3. Yamashino T, et al.
    A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(6): p. 619-29
    [PMID:12826627]
  4. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
    [PMID:12897250]
  5. Bailey PC, et al.
    Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana.
    Plant Cell, 2003. 15(11): p. 2497-502
    [PMID:14600211]
  6. Rizhsky L, et al.
    When defense pathways collide. The response of Arabidopsis to a combination of drought and heat stress.
    Plant Physiol., 2004. 134(4): p. 1683-96
    [PMID:15047901]
  7. Khanna R, et al.
    A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors.
    Plant Cell, 2004. 16(11): p. 3033-44
    [PMID:15486100]
  8. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
    [PMID:16920880]
  9. Franklin KA,Whitelam GC
    Light-quality regulation of freezing tolerance in Arabidopsis thaliana.
    Nat. Genet., 2007. 39(11): p. 1410-3
    [PMID:17965713]
  10. Davi
    Transcriptional factor interaction: a central step in DELLA function.
    Curr. Opin. Genet. Dev., 2008. 18(4): p. 295-303
    [PMID:18590820]
  11. Penfield S,Josse EM,Halliday KJ
    A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy.
    Plant Mol. Biol., 2010. 73(1-2): p. 89-95
    [PMID:19911288]
  12. Gallego-Bartolomé J, et al.
    Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis.
    Mol. Biol. Evol., 2010. 27(6): p. 1247-56
    [PMID:20093430]
  13. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  14. Richter R,Behringer C,M
    The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS.
    Genes Dev., 2010. 24(18): p. 2093-104
    [PMID:20844019]
  15. Toettcher JE,Gong D,Lim WA,Weiner OD
    Light control of plasma membrane recruitment using the Phy-PIF system.
    Meth. Enzymol., 2011. 497: p. 409-23
    [PMID:21601096]
  16. Bu Q,Castillon A,Chen F,Zhu L,Huq E
    Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis.
    Plant Mol. Biol., 2011. 77(4-5): p. 501-11
    [PMID:21928113]
  17. R
    Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes.
    Plant Cell, 2012. 24(11): p. 4360-75
    [PMID:23192226]
  18. Sairanen I, et al.
    Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4907-16
    [PMID:23209113]
  19. Dong J, et al.
    Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark.
    Plant Cell, 2014. 26(9): p. 3630-45
    [PMID:25248553]
  20. Qiu Y, et al.
    HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.
    Plant Cell, 2015. 27(5): p. 1409-27
    [PMID:25944101]